Surprise, Cupcake, Buttons, Gusty, Fizzy, Baby Cuddles, and Spike are on their way to Flutter Valley for a celebration. They're already late, and if the Witches from the Volcano of Gloom have anything to say about it, they'll never get there. Hydia, Reeka, and Draggle are watching the ponies in the viewing pool and Hydia is vowing her revenge on the Flutter Ponies for previously destroying the Smooze. Hydia sends her daughters, who actually want to help, to first stop the Little Ponies from getting to Flutter Valley. Reeka tries to use a spell to make a lasso to trap the ponies.

Hydia sees this and is proud until Honeysuckle, Lily, Morning Glory, and Forget-Me-Not show up and using their Utter Flutter, blow Reeka and Draggle away. But Reeka decides that rather then face Hydia, she and Draggle go to Flutter Valley and try again.

In Flutter Valley, Rosedust, the Queen of the Flutter Ponies declares today Sun Tuesday as she and the Flutter Ponies worship not only the sun, but also their Sunstone which is responsible for bringing the sunlight to their valley which was formerly baron and lifeless.

But Reeka has an idea to bury Flutter Valley and the ponies and Bushwoolies in a landslide. They nearly succeed but the landslide backfires and throws mud the the witches. Giving up, Reeka and Draggle go home. Honeysuckle in not satisfied with just letting them go, but Morning Glory doesn't think revenge is necessary. The Little Ponies say good-bye and walk home with the Bushwoolies.

Back at the Volcano, Hydia can't take anymore incompetence from her daughters. As punishment, she forces them to eat donuts and then has a family meeting to try to get some new ideas. She consults portraits to her long-since dead relatives who come to life and they tell her to seek out Bumble and her Bees to steal the Sunstone, which would cause Flutter Valley to die.

The witches would then take over Flutter Valley which would be just the way they like it. While walking through Bumbleland, they remember know how nasty the Bees have become ever since they got kicked out of Flutter Valley and dumped in this freezing land. They are attacked by a swarm of Bees and takes to Bumble. Reeka and Draggle propose that Bumble steal the Sunstone and use it's power to direct the sun to allow plants and flowers to grow in Bumbleland. Bumble agrees realizing that she would no longer have to import flowers containing her delicious nectar.

On their way home, the little ponies encounter little furry creatures called Furbobs who are first cousins to the Bushwoolies. The Furbobs, who never agree with each other, agreed when they mentioned why they can't remember where they lived.

They were chased away by the Stonebacks, wild reptiles who attacked again that very moment. They destroy a bridge, and when the ponies fall, Baby Cuddles hurts her leg and can't walk. The Furbobs take her to their home to help her. In Flutter Valley, the witches distract the Flutter Ponies while Bumble and her Bees steal the Sunstone. While pursuing the bees, Bumble traps the Flutter Ponies an a giant, sticky honeycomb. She orders honey poured into it, that covers the Flutter Ponies' wings, keeping them from flying out. Bumble has Sting set up the Sunstone to immediately begin reflecting the sun. Bumble decides that the Flutter Ponies will be her slaves. At the same time, Flutter Valley begins to wilt, and the witches move in and by sunset, it would remain that way.

Morning Glory makes it out of the honeycomb and searches for help. But her wings are still to heavy, and she is recaptured. She is placed in a cage with Sting personally guarding her.

She tries to explain the situation with the Sunstone and Flutter Valley to him, but he doesn't care. But when Morning Glory asks Sting if he would rather be flying and playing instead of working for Bumble, he starts to cry. He admits that he can't fly and that he never learned because he was never good at it. Morning Glory encourages him to try again, and when he learns, he becomes friends with her. But he still keeps her in the cage. In Furbobia, the Furbobs use their steamer to heal Baby Cuddles' leg with music and the power of nature. To thank the Furbobs, the Little Ponies return to Flutter Valley to ask the Flutter Ponies to help then with the Stonebacks problem. But when they get there, Flutter Valley is nearly baron and the witches soon capture them; including Surprise who originally stayed in Furbobia.

In Bumbleland, the Sunstone is being overused, causing it burn the plants and flowers. Bumble ignores Pointer's warning until the Sunstone turns red and Bumbleland catches fire. The bees try to extinguish the fire, but when it becomes too overwhelming, the abandon Bumbleland until the fire burns out. From above, Sting notices the fire, and that the bees are gone. Not even to save the Flutter Ponies, Sting refuses to let Morning Glory go. But when he learns that Bumble left them behind, he and Morning Glory decide to save the Flutter Ponies themselves. Sting knocks the Sunstone into the ground, stopping thee heat but losing the Sunstone.

Inside the honeycomb, the Flutter Ponies feel the heat and use it to melt the honey from their wings. They are finally strong enough to break out just as Bumble returns to face Sting. He sides with the Flutter Ponies and he and Morning Glory set out on their own to search for Megan on the other side of the Rainbow. The Flutter Ponies are quickly recaptured since their wings were still too heavy to fly away.

In Flutter Valley, Fizzy puts the Furbob in a bubble and gives him to Aagh as a toy. But the bubble breaks and the Furbob runs for help. When Sing and Morning Glory reach Megan's farm, they don't find her until she has to save them from a runaway bull they accidentally let loose. She returns with them to Ponyland to try to help.

In Flutter Valley, Draggle is about the cast a spell to turn the ponies entirely purple. But when it backfires and covers her, Reeka, Hydia, and Aagh's claw, she's in big trouble. Hydia, Reeka, and Aagh go back to Volcano of Gloom and leave Draggle with the ponies. Meantime, the poor Furbob is too confused to decide where he can go to find help. From the air, Megan, Sting, and Morning Glory spot him. Together, they decide to go to Bumbleland to first get the Sunstone and free the Flutter Ponies. But the Flutter Ponies have been enslaved by Bumble and are forced to dig for the Sunstone. While trying to escape, Honeysuckle is knocked into the hole they were digging. The others are recaptured along with Megan, Sting, Morning Glory, and the Furbob.

In Flutter Valley, the ponies trick Draggle into letting them glow by pretending to teach her how to do their magic. But they're soon back in the net when Hydia, Reeka, and Aagh return to punish Draggle. In Bumbleland. Honeysuckle crawls out, and she tells everyone it's safe down there. The Stonebacks follow her out and everyone escapes down the hole. Inside, they fill is the entrance to the hole to keep the bees out.

But the Furbob still doesn't feel safe since he's stuck in the hole with the Stonebacks. Megan convinces him that even though the Stonebacks can't talk, they are trying to communicate in order to be friends. Sting and the Flutter Ponies cool the Sunstone with their wings. Once it's cool, the Stonebacks lead everyone to Flutter Valley underground. But Bumble and her Bees are also on their way there to reclaim the Sunstone. When Megan and the others arrive, they are blocked by Aagh, who plans to keep them out until after the sun has set. Megan tries a trick she learned from Molly the last time they ran into Aagh. She gets everyone to tickle him, but they soon find out that Hydia gave him something to keep him from bring ticklish. Next, the Stonebacks help by digging a tunnel under Aagh and they all follow them into the Valley with the help of Baby Cuddles, Cupcake, the Furbobs, and the Bushwoolies who just arrived. Just as the sun begins to set, the Flutter Ponies attack the witches free the trapped ponies and they set the Sunstone in place.

But just then, the Boos arrive and Sting tries to stop Bumble. Rosedust intervenes and offers that if Bumble leaves the Flutter Ponies alone, she can come to Flutter Valley and take flowers anytime. She agrees, and Sting returns to Bumbleland with her and the other bees.

The Sunstone begins reflecting the sun, revitalizing Flutter Valley...but not before the witches block the sun with a dark cloud. But they are no match for the Flutter Ponies' Utter Flutter and they blow the cloud and with witches back to the Volcano of Gloom , finally defeating them. As the sun reappears, the rest of the valley is replenished and the ponies and their friends celebrate the rebirth of Flutter Valley.